Freesurfer June 2011

freesurfer@nmr.mgh.harvard.edu

118 participants
168 discussions

Whole brain parcellation.
by Sudhin A. Shah 10 Jun '11

10 Jun '11

Hello, I am a beginner so please bear with me. I want to obtain binary masks for every region (Cortical + subcortical). I am using FSL(feat) to do this BUT am not sure what the labels would be. I have looked at FreeSurferColorLUT.txt for aparc+aseg-in-highres.mgz BUT do not know which labels to use to avoid overlap and ensure full coverage. Thank you, S

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MEMPR and longitudinal processing stream
by Thomas, Adam (NIH/NIMH) [E] 10 Jun '11

10 Jun '11

When using MEMPR images (Van der Kouwe et al., 2008) in the longitudinal processing stream, when should the dura correction (mris_makes_surfaces -dura) be ran? After the first cross-sectional run of recon-all, after the final longitudinal run of recon-all, or maybe both? I have the same question with respect to the "-hippo-subfields" flag. Should this flag be specified on each run of recon-all in the longitudinal processing stream? Thanks, -Adam

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mri_cvs_register update
by Lilla Zollei 10 Jun '11

10 Jun '11

Hi, We found a bug in the mri_cvs_register script after the release. Please, download the new version of applyMorph and mri_cvs_register from one of the below links for Linux Centos4, Linux Centos4 x86 64 and Mac Leopard respectively: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/mac-leopard-intel --Lilla

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Optimization ITI
by daniel geisler 10 Jun '11

10 Jun '11

Dear Freesurfers, We intend to implement a probabilistic reversal learning task (Hampton et al, 2006) in an ER-design. Each of its 120 trials matches the following pattern: |<---- Response ---->|<-- Fixation -->|<-- Feedback -->| The phases of Response and Feedback take 2 sec and 1 sec, respectively. We are wondering how to setup the durations of Fixation and the ITI in an optimal way, which means trading task-duration off against efficiency. We would like to estimate these values by some software rather than by rule of thumb. Do you know whether there is such a tool anyway? In Freesurfer there is a tool included that is called optseq2. It is described as follows: “optseq2 is a tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be. RPER is also more efficient than fixed-interval event related (FIER) because more stimuli can be presented within a given scanning interval at the cost of assuming that the overlap in the hemodynamic responses will be linear. In SPM parlance, RPER is referred to as 'stochastic design'. The flexibility of RPER means that there are a huge number of possible schedules, and they are not equal. optseq2 randomly samples the space of possible schedules and returns the 'best' one, where the user can control the definition of 'best'. Cost functions include: average efficiency, average variance reduction factor (VRF), and a weighted combination of average and stddev of the VRF. The user can also specify that the first order counter-balancing of the sequence of event-types be pre-optimized.” Will it do the job? After a first try, I guess that optseq2 may not allow constraints such that Response is always followed by Feedback. Could you please give me a hint how to setup durations of Fixation and the ITI in an optimal way? Best wishes from Dresden, Daniel ::::::::::::::::::::::::::::::::::::::::: Dipl.-Inf. Daniel Geisler Wissenschaftlicher Mitarbeiter Bereich Angewandte Entwicklungsneurowissenschaften Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie Tel. +49 (0)351 458-7071 Fax +49 (0)351 458-7206 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74 (Haus 25, Raum 233A), 01307 Dresden http://www.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 201 145 00020

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Phillips 3T
by Ayaz, Muhammad 10 Jun '11

10 Jun '11

Dear All, I have T1 images single scan from Phillips 3T. Images quality looks good. Since we use 8 channel should I be collecting 2 data set to average or single data will be sufficient? Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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Tracula question: trac-all config file and number of B0 specification
by Deryk S. Beal, Ph.D. 10 Jun '11

10 Jun '11

Dear Tracula Users Does Tracula assume that the number of B0 scans, specified in Step 7.3 of the config file tutorial (below), are the first X number of volumes in the 4Dnii.gz file or will the Tracula routines know from the bvals file where the B0 scans are ordered in the file? For example, I have two runs of 16 directions + 2 B0s each for each of my subjects. I have merged the two runs together and the resulting file has the volumes ordered such that the bvals are entered into Tracula as follows: 0 0 1000 1000 1000 etc 0 0 1000 1000 1000 etc My question pertains to the following part of the Tracula config file: *Step7.3: Specifying Number Of low-b Images* The last step to set up if not using original DICOMs would be to specify the number of low-b images with the following variable: set nb0 = *No. of low-b images* Thank you in advance for your help. Cheers, Deryk Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO Speech-Language Pathologist C.I.H.R. Post Doctoral Research Fellow Department of Cognitive and Neural Systems Speech Laboratory Boston University, 677 Beacon Street, Boston, MA 02215 dsbeal(a)bu.edu http://blogs.bu.edu/dsbeal/about/ ************************************************************************* This email may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by others is strictly prohibited. If you have received this email in error, please contact the sender and delete all copies. Opinions, conclusions or other information expressed or contained in this email are not given or endorsed by the sender unless otherwise affirmed independently by the sender.

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MRIs processed with two different FS versions
by Yolanda Vives 10 Jun '11

10 Jun '11

Dear Freesurfers, I have a dataset processed with a classical recon-all of Freesurfer v.4.3.1 and there are two MRIs that were not segmented correctly due to the register. After several unsuccessful attempts to improve this step using tkregister2, finally I have successfully processed them with FS v5.0. Would it be correct to perform a QDEC analysis to analyse cortical thickness using all my dataset (mixing MRIs processed with FS 4.3.1 and two of them processed with FS 5.0) ? Thank you for your help, Yolanda

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functional mask conversion from talairach space
by Sam Cartmell 09 Jun '11

09 Jun '11

Hello Freesurfers, Using FS 4.5, I am attempting to do an ROI analysis based on activations seen in the group contrast. I'd like these ROI's to be a sphere around the peak voxel of each activation. Using a matlab program written by a colleague, I was able to generate spherical masks around the peak voxel in talairach functional space (i.e. no registration file is needed to view these masks overlayed on fsaverage and the masks have dimension 76 x 76 x 93 and voxel size 2 x 2 x 2 mm). I'd like to transfer these masks to native functional space (the same space as each subject's beta.nii file) so that I might extract the timecourse activity in matlab, and I was wondering 1) if what I list below is a valid way to do this transformation, and 2) if there is an alternative/superior way to accomplish this. After a lot of experimenting, the following series of commands appears to work: 1. mri_convert --input_volume group_sphere_mask.nii.gz --output_volume output1.nii.gz --ait Subject/mri/transforms/talairach.xfm --this gives me an error message: ERROR MSGS -- INFO: Trying to get the source volume information from the transform name corRead(): can't open file Subject/mri/transforms/../orig/COR-.info INFO: Failed to find Subject/mri/transforms/../orig as a source volume. The inverse c_(ras) may not be valid. 2. mri_vol2vol --mov output1.nii.gz --targ Subject/bold/004/f.nii --regheader --o output2.nii.gz --interp nearest --this gives me a file with the right dimensions, but the values in the mask are no longer = 1, so then I use 3. mri_binarize -i output2.nii.gz -o output3.nii.gz --min .02 --where the min is a somewhat arbitrary threshold that seems to capture most of the voxels that were in the mask When I overlay this file on the subjects anatomical using: tkmedit Subject orig.mgz -overlay output3.nii.gz --reg Subject/bold/register.dat I get a mask which seems to be in the right place, but is no longer truly spherical and has the occasional voxel dropped from from the mask I would be any methods which might preserve the spherical shape and/or prevent any voxel dropout (and doesn't give me error messages). Thanks, Sam Cartmell Research Assistant Visual Cognitive Neuroscience Laboratory, Dept Psychology Yale University

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Regarding: "mri_segstats error"
by Joel Bruss 09 Jun '11

09 Jun '11

I ran across the same issue reported in: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17687.html The initial question was why mri_segstats did not work and complained: "Error: could not open stats/aseg/stats for writing" If you try to, literally, copy and paste the same command listed in the aseg.stats file: mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --inintensity-name norm--in-intensity-units MR --etiv --subject 004 you'll get the error message, even if you source the freesurfer setup file (/usr/freesurfer/SetUpFreeSurfer.csh). In order to run the command, one needs to type out the complete path to each referenced file: mri_segstats --seg ${SUBJECTS_DIR}/'subject"/mri/aseg.mgz --sum ${SUBJECTS_DIR}/'subject"/stats/aseg.stats --pv ${SUBJECTS_DIR}/'subject"/mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask ${SUBJECTS_DIR}/'subject"/mri/brainmask.mgz --in ${SUBJECTS_DIR}/'subject"/mri/norm.mgz --inintensity-name norm--in-intensity-units MR --etiv --subject 004 (obviously replace ${SUBJECTS_DIR}/'subject" with the correct path and subject ID). I apologize for the lengthy response but I felt the referenced thread ended without truly addressing the problem. Also, when running into the exact same error I was left scratching my head trying to figure it out. Hopefully someone else finds this useful.

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Re: [Freesurfer] Middle line issue
by Wayne Su 09 Jun '11

09 Jun '11

Anybody can help me out? What caused the middle line (both pial and wm boundary) shifted to right side even the wm mask is good? Please see the attached images. Thank you very much. Wayne On 07/06/11 2:58 PM, "Wayne Su" <wsu(a)interchange.ubc.ca> wrote: > > >> Hello, >> I have a subject with very big ventricle. I managed to edit wm.mask and >> aseg.mgz, and rerun the recon-all autorecon2, but the middle line separating >> left/right ventricles is still not right (attached). Is there any way to >> correct it? I¹m using FS 5.1. Thanks. >> >> Wayne >>> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail.

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Freesurfer June 2011